Alignments for a candidate for adiA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Shewanella amazonensis SB2B

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 6937822 Sama_1963 arginine decarboxylase (RefSeq)

Query= BRENDA::Q7MK24
         (640 letters)



>FitnessBrowser__SB2B:6937822
          Length = 636

 Score =  868 bits (2244), Expect = 0.0
 Identities = 424/631 (67%), Positives = 513/631 (81%), Gaps = 1/631 (0%)

Query: 11  LDRVRADYNVHYWSQGFYGIDDQGEMYVSPRSDN-AHQIQLSKIVKQLEERQLNVPVLVR 69
           +D  RA YNV +WSQGFYGI D+GE+ VSP   N   +I L+ + K + +  +++PVLVR
Sbjct: 6   IDDARAGYNVAHWSQGFYGISDEGEVTVSPDPKNPTFKIGLNALAKDMVKAGVSLPVLVR 65

Query: 70  FPQILHQRVHSICDAFNQAIEEYQYPNKYLLVYPIKVNQQREVVDEILASQAQLETKQLG 129
           FPQILH RV  +C  FNQAI++Y+Y + YLLVYPIKVNQQ+ VV+EILASQ      QLG
Sbjct: 66  FPQILHHRVDHLCQMFNQAIQKYEYQSDYLLVYPIKVNQQQTVVEEILASQVSKTVPQLG 125

Query: 130 LEAGSKPELLAVLAMAQHASSVIVCNGYKDREYIRLALIGEKLGHKVFIVLEKMSELDLV 189
           LEAGSKPEL+AVLAMAQ ASSVIVCNGYKD+EYIRLALIGEKLGH V+IVLEKMSEL +V
Sbjct: 126 LEAGSKPELMAVLAMAQKASSVIVCNGYKDKEYIRLALIGEKLGHSVYIVLEKMSELQMV 185

Query: 190 LREAKSLGVTPRLGIRIRLASQGAGKWQASGGEKSKFGLSASQVLNVISRLKKENQLDTL 249
           L E+K LGVTPRLG+R RLA QG GKWQASGGEKSKFGLSA+Q+L V+ RLK E+ L++L
Sbjct: 186 LEESKKLGVTPRLGLRARLAFQGKGKWQASGGEKSKFGLSAAQILKVVERLKDEDMLESL 245

Query: 250 QLVHFHLGSQMANIRDVRNGVNESARFYCELRTLGANITYFDVGGGLAIDYDGTRSQSSN 309
           QL+HFHLGSQ+ANIRD+R+GV E+ARFYCELR LGA +  FDVGGGLA+DYDGTRSQS+N
Sbjct: 246 QLLHFHLGSQIANIRDIRHGVGEAARFYCELRKLGAKVNCFDVGGGLAVDYDGTRSQSNN 305

Query: 310 SMNYGLVEYARNIVNTVGDVCKDYKQPMPVIISESGRSLTAHHAVLISNVIGTETYKPET 369
           SMNY L EYA NIV+ + DVC   +QPMP IISESGR LTAHHAVLI++VIGTE Y PE 
Sbjct: 306 SMNYALAEYANNIVSVLTDVCNQNEQPMPRIISESGRYLTAHHAVLITDVIGTEAYSPED 365

Query: 370 VTEPEEDFPLLLNNMWRSWLNLHNGTDARALIEIYNDTQSDLAEVHSQFATGVLTLEHRA 429
           +  PEE+ P LL+NMWRSW  + +  D RALIEI++DTQSDLAE  S FA G L+LE RA
Sbjct: 366 IPAPEEEAPQLLHNMWRSWNEISSRLDQRALIEIFHDTQSDLAEAQSLFALGQLSLEDRA 425

Query: 430 WAEQTSLRIYYELNRLMSTKNRFHRPILDELSERLADKFFVNFSLFQSLPDSWGIDQVFP 489
           WAEQ +L + +EL  LM+ +NR+ RPI+DEL+E+LAD+FFVNFSLFQSLPD+WGIDQVFP
Sbjct: 426 WAEQCNLAVCHELQGLMNARNRYQRPIIDELNEKLADRFFVNFSLFQSLPDAWGIDQVFP 485

Query: 490 VLPLSGLQNAADRRAVMLDITCDSDGAIDAYVDGQGIESTLPVPAWNEDEPYLMGFFLVG 549
           VLPLSGL    +RRAVMLDITCDSDG +D YVDGQGIE+TLPVP W+ ++PYL+GFFLVG
Sbjct: 486 VLPLSGLDKVPERRAVMLDITCDSDGIVDQYVDGQGIETTLPVPNWSAEDPYLIGFFLVG 545

Query: 550 AYQEILGDMHNLFGDTHSVVVNVGDQGEINIDFINEGDTVEDMMRYVHIDVDQIRKNYHS 609
           AYQEILGD+HNLFGDT+S VV + ++G+ NI+ +  GDTV D++RYV++D     + Y  
Sbjct: 546 AYQEILGDLHNLFGDTNSAVVRIDEEGQTNIESVLAGDTVADVLRYVNLDAVSFMRTYEE 605

Query: 610 LVSQRVDQEEQQQILAELEQGLSGYTYLEDF 640
           LV+  + ++E+  IL EL+ GL GYTYLEDF
Sbjct: 606 LVNSHIAEDERAMILEELQVGLKGYTYLEDF 636


Lambda     K      H
   0.318    0.135    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1118
Number of extensions: 47
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 640
Length of database: 636
Length adjustment: 38
Effective length of query: 602
Effective length of database: 598
Effective search space:   359996
Effective search space used:   359996
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate 6937822 Sama_1963 (arginine decarboxylase (RefSeq))
to HMM TIGR01273 (speA: arginine decarboxylase (EC 4.1.1.19))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01273.hmm
# target sequence database:        /tmp/gapView.5125.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01273  [M=624]
Accession:   TIGR01273
Description: speA: arginine decarboxylase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.3e-266  869.5   0.0   8.2e-266  869.3   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937822  Sama_1963 arginine decarboxylase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937822  Sama_1963 arginine decarboxylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  869.3   0.0  8.2e-266  8.2e-266       1     624 []       4     634 ..       4     634 .. 0.98

  Alignments for each domain:
  == domain 1  score: 869.3 bits;  conditional E-value: 8.2e-266
                         TIGR01273   1 wsaeesakvYnikgWgagyfavnkeGevsvrpkgeetlkeidllelvkqveakglklPllvrFpdilqkrikslnaa 77 
                                       ws++++++ Yn+++W++g++ + +eGev+v+p+ ++ + +i l +l k++ ++g++lP+lvrFp+il++r+++l++ 
  lcl|FitnessBrowser__SB2B:6937822   4 WSIDDARAGYNVAHWSQGFYGISDEGEVTVSPDPKNPTFKIGLNALAKDMVKAGVSLPVLVRFPQILHHRVDHLCQM 80 
                                       889999*********************************************************************** PP

                         TIGR01273  78 FkeaieeleYaskyqavyPiKvnqqrevveelvasg....gkslGLEaGsKpEllialalaekpkavivcnGyKDre 150
                                       F++ai+++eY+s+y +vyPiKvnqq++vvee++as+      +lGLEaGsKpEl+++la+a+k+++vivcnGyKD+e
  lcl|FitnessBrowser__SB2B:6937822  81 FNQAIQKYEYQSDYLLVYPIKVNQQQTVVEEILASQvsktVPQLGLEAGSKPELMAVLAMAQKASSVIVCNGYKDKE 157
                                       **********************************9986444589********************************* PP

                         TIGR01273 151 yielaliarklglkvviviekleEldlvieeakklgvkPklGlRvrLaskgsgkwassgGeksKFGLsasqvlevvk 227
                                       yi+lali++klg+ v+iv+ek++El++v+ee+kklgv+P+lGlR+rLa +g gkw+ sgGeksKFGLsa+q+l+vv+
  lcl|FitnessBrowser__SB2B:6937822 158 YIRLALIGEKLGHSVYIVLEKMSELQMVLEESKKLGVTPRLGLRARLAFQGKGKWQASGGEKSKFGLSAAQILKVVE 234
                                       ***************************************************************************** PP

                         TIGR01273 228 klkeedlldslkllHfHlGsqianiddvkkgvrEaarlyvelrklGvkievvdvGGGLgvdYdGtksksdlsvnYsl 304
                                       +lk+ed+l+sl+llHfHlGsqiani+d+++gv Eaar+y+elrklG+k++++dvGGGL+vdYdGt+s+s++s+nY l
  lcl|FitnessBrowser__SB2B:6937822 235 RLKDEDMLESLQLLHFHLGSQIANIRDIRHGVGEAARFYCELRKLGAKVNCFDVGGGLAVDYDGTRSQSNNSMNYAL 311
                                       ***************************************************************************** PP

                         TIGR01273 305 eeyaaavvaalkevceekgvpePviisEsGRaitahhavlvaevleveeeeeeeaeeileeeapeevk....eleel 377
                                        eya+++v++l +vc+++++p P+iisEsGR++tahhavl+++v+++e+++ e+++++ e eap++++    +++e+
  lcl|FitnessBrowser__SB2B:6937822 312 AEYANNIVSVLTDVCNQNEQPMPRIISESGRYLTAHHAVLITDVIGTEAYSPEDIPAPEE-EAPQLLHnmwrSWNEI 387
                                       *****************************************************9999766.9999999888889*** PP

                         TIGR01273 378 lkeideesaeelledavqlleeavelfklGkldleeralaeqlalailkkvke.leakekshreildelqeklaeky 453
                                       ++ +d+++++e+++d++++l+ea +lf+lG+l+le+ra+aeq+ la++++++  ++a+++ +r+i+del+ekla+++
  lcl|FitnessBrowser__SB2B:6937822 388 SSRLDQRALIEIFHDTQSDLAEAQSLFALGQLSLEDRAWAEQCNLAVCHELQGlMNARNRYQRPIIDELNEKLADRF 464
                                       *****************************************************999********************* PP

                         TIGR01273 454 lvnlslFqslPDaWgidqlfPilPlerLdekpdrravllDltCDsDGkikkfveeqgiektlplheldkdeeyllgf 530
                                       +vn+slFqslPDaWgidq+fP+lPl++Ld+ p+rrav+lD+tCDsDG ++++v++qgie+tlp+++++ +++yl+gf
  lcl|FitnessBrowser__SB2B:6937822 465 FVNFSLFQSLPDAWGIDQVFPVLPLSGLDKVPERRAVMLDITCDSDGIVDQYVDGQGIETTLPVPNWSAEDPYLIGF 541
                                       ***************************************************************************** PP

                         TIGR01273 531 flvGAYqEiLgdvHnLFgdteavevvvkekgeveveaieegdtvedvlkavqydpeellkalkqkvaeaklkaeekk 607
                                       flvGAYqEiLgd HnLFgdt+++ v ++e+g++++e++  gdtv+dvl++v++d+   ++++++ v++ +++++e++
  lcl|FitnessBrowser__SB2B:6937822 542 FLVGAYQEILGDLHNLFGDTNSAVVRIDEEGQTNIESVLAGDTVADVLRYVNLDAVSFMRTYEELVNS-HIAEDERA 617
                                       *****************************************************************888.699***** PP

                         TIGR01273 608 qvlelleaglsgypYLs 624
                                       ++le+l++gl+gy+YL+
  lcl|FitnessBrowser__SB2B:6937822 618 MILEELQVGLKGYTYLE 634
                                       ***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (624 nodes)
Target sequences:                          1  (636 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.90
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources